vestnik-bio-msuВестник Московского университета. Серия 16. БиологияVestnik Moskovskogo universiteta. Seriya 16. Biologiya0137-0952Lomonosov Moscow State University, School of Biology10.55959/MSU0137-0952-16-80-2-4vestnik-bio-msu-1507Research ArticleОРИГИНАЛЬНОЕ ИССЛЕДОВАНИЕRESEARCH ARTICLEМолекулярное моделирование взаимодействия метиленового синего с виропорином коронавируса SARS-CoV-2Molecular modeling of the methylene blue interaction with the SARS-CoV-2 coronavirus viroporinhttps://orcid.org/0000-0003-0972-9378ВасюченкоЕ. П.VasyuchenkoE. P.

Васюченко Екатерина Павловна – аспирант кафедры биофизики биологического факультета МГУ

Тел.: 8-495-939-11-16

119234, г. Москва, Ленинские горы, д. 1, стр. 12

80000, г. Псков, площадь Ленина, д. 2

Leninskie gory 1–12, Moscow, 119234

 Lenin square 2, Pskov, 180000

vasyuchenko.katya@gmail.comhttps://orcid.org/0000-0002-5918-5084ХолинаЕ. Г.KholinaE. G.

Холина Екатерина Георгиевна – канд. биол. наук, ст. преп. кафедры биофизики

Тел.: 8-495-939-11-16

119234, г. Москва, Ленинские горы, д. 1, стр. 12

Leninskie gory 1–12, Moscow, 119234

tenarra@mail.ruhttps://orcid.org/0000-0002-9397-1548ФедоровВ. А.FedorovV. A.

Федоров Владимир Андреевич – канд. физ.-мат. наук, науч. сотр. кафедры биофизики

Тел.: 8-495-939-11-16

119234, г. Москва, Ленинские горы, д. 1, стр. 12

Leninskie gory 1–12, Moscow, 119234

xbgth@yandex.ruhttps://orcid.org/0000-0002-4571-0431СтраховскаяМ. Г.StrakhovskayaM. G.

Страховская Марина Глебовна – докт. биол. наук, доц. кафедры синтетической биологии

Тел.: 8-495-938-00-06

119234, г. Москва, Ленинские горы, д. 1, стр. 12

Leninskie gory 1–12, Moscow, 119234

maristra@yandex.ruhttps://orcid.org/0000-0002-4949-6591КоваленкоИ. Б.KovalenkoI. B.

Коваленко Илья Борисович – докт. физ.-мат. наук, вед. науч. сотр. кафедры биофизики

Тел.: 8-495-939-11-16

119234, г. Москва, Ленинские горы, д. 1, стр. 12

Leninskie gory 1–12, Moscow, 119234

ikovalenko78@gmail.comhttps://orcid.org/0000-0001-8354-7965РубинА. Б.RubinA. B.

Рубин Андрей Борисович – академик РАН, докт. биол. наук, зав. кафедрой биофизики

Тел.: 8-495-939-11-16

119234, г. Москва, Ленинские горы, д. 1, стр. 12

Leninskie gory 1–12, Moscow, 119234

rubin@biophys.msu.ruБиологический факультет, Московский государственный университет имени М.В. Ломоносова; Научно-образовательный математический центр «Северо-Западный центр математических исследований имени Софьи Ковалевской», Псковский государственный университетРоссияSchool of Biology, Lomonosov Moscow State University; Scientific and Educational Mathematical Center “Sofia Kovalevskaya Northwestern Center for Mathematical Research,” Pskov State UniversityRussian FederationБиологический факультет, Московский государственный университет имени М.В. ЛомоносоваРоссияSchool of Biology, Lomonosov Moscow State UniversityRussian Federation20251407202580296104Copyright © Васюченко Е.П., Холина Е.Г., Федоров В.А., Страховская М.Г., Коваленко И.Б., Рубин А.Б., 20252025Васюченко Е.П., Холина Е.Г., Федоров В.А., Страховская М.Г., Коваленко И.Б., Рубин А.Б.Vasyuchenko E.P., Kholina E.G., Fedorov V.A., Strakhovskaya M.G., Kovalenko I.B., Rubin A.B.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://vestnik-bio-msu.elpub.ru/jour/article/view/1507

Виропорины являются небольшими мембранными белками оболочечных вирусов. Они играют важную роль как в жизненном цикле вируса, так и развитии патогенеза заболевания. В связи с этим, ингибирование виропоринов считается перспективной стратегией в лечении многих заболеваний, вызванных оболочечными вирусами, такими как коронавирус, вирус герпеса, вирус иммунодефицита человека, вирус Эбола и многие другие. Важным этапом поиска высокоэффективных ингибиторов таких каналов является изучение особенностей взаимодействия потенциальных противовирусных препаратов с аминокислотными остатками канала виропорина. В свою очередь, метиленовый синий является известным эффективным противовирусным агентом и широко применяется в медицинской практике. В данной работе мы провели расчеты молекулярной динамики взаимодействия метиленового синего с каналом виропорина коронавируса SARS-CoV-2 методом отбора зонтичных проб. Анализ образуемых контактов между молекулой метиленового синего и аминокислотными остатками виропорина показал, что ключевую роль в связывании играют нековалентные стэкинг-взаимодействия между системой ароматических колец метиленового синего и остатками фенилаланина, расположенными в центре канала виропорина. Полученные результаты приближают нас к пониманию механизмов противовирусного действия метиленового синего. Проведение подобных вычислительных экспериментов представляется эффективным подходом при поиске ингибиторов виропоринов.

Viroporins are small membrane proteins of enveloped viruses. They play an important role both in the life cycle of the virus and in the development of disease pathogenesis. In this regard, inhibition of viroporins is considered a promising strategy in the treatment of many diseases caused by enveloped viruses, such as coronavirus, herpes virus, human immunodeficiency virus, Ebola virus and many others. An important step in the search for highly effective inhibitors of such channels is the study of the interaction of potential antiviral drugs with the amino acid residues of the viroporin channel. In turn, methylene blue is a well-known effective antiviral agent and is widely used in medical practice. In this work, we carried out molecular dynamic calculations of the interaction of methylene blue with the viroporin channel of the SARS-CoV-2 coronavirus using the umbrella sampling method. Analysis of the contacts formed between the methylene blue molecule and the amino acid residues of viroporin showed that the key role in binding is played by non-covalent stacking interactions between the system of aromatic rings of methylene blue and the phenylalanine residues located in the center of the viroporin channel. The results obtained bring us closer to understanding the mechanisms of the antiviral action of methylene blue. Conducting such computational experiments seems to be an effective approach in the search for viroporin inhibitors.

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The authors declare that there are no conflicts of interest present.